Comparison of four methods used in ComPath. The performance comparison of Whole-HMM search, CSR-HMM search, PDB-domain search, and FASTA search methods in terms of sensitivity and specificity. Glucolysis/Gluconeogenesis pathway (Pathway ID: 00010) and five reference genomes were selected: Escherichia coli K12 (NC_00913), Haemophilus influenzae (NC_000907), and Salmonella typhimurium LT2 (NC_003197) from Proteobacteria; and Bacillus anthracis str. Ames (NC_003997) and Bacillus halodurans C-125 (NC_002570) from Firmicutes. Three well-annotated genomes (Salmonella enterica subsp. enterica serovar Typhi Ty2,, Vibrio cholerae O1 biovar eltor str. N16961 chromosome II (NC_002506), and Yersinia pestis CO92 (NC_003134) were selected as query genomes to accurately evaluate performance of the four prediction methods. The plots show sensitivity and specificity of the four methods. See also Table 2.